This directory contains a dump of the UCSC genome annotation database for
the Mar. 2012 (Baylor Panu_2.0/papAnu2) assembly of the baboon genome (papAnu2, Baylor College of Medicine).
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
http://www.ncbi.nlm.nih.gov/genome/394
http://www.ncbi.nlm.nih.gov/genome/assembly/383538
http://www.ncbi.nlm.nih.gov/bioproject/54005
Files included in this directory (updated nightly):
- *.sql files: the MySQL commands used to create the tables
- *.txt.gz files: the database tables in a tab-delimited format
compressed with gzip.
To see descriptions of the tables underlying Genome Browser annotation
tracks, select the table in the Table Browser:
http://genome.ucsc.edu/cgi-bin/hgTables?db=papAnu2
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
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If you plan to download a large file or multiple files from this
directory, we recommend you use ftp rather than downloading the files
via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to
the directory goldenPath/papAnu2/database/. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Alternate methods to ftp access.
Using an rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/papAnu2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/papAnu2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/papAnu2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/papAnu2/database/gc5BaseBw.txt.gz'
-O gc5BaseBw.txt.gz
Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.cse.ucsc.edu/gbdb/
To uncompress the *.txt.gz files:
gunzip <table>.txt.gz
The tables can be loaded directly from the .txt.gz compressed file.
It is not necessary to uncompress them to load into a database,
as shown in the example below.
To load one of the tables directly into your local mirror database,
for example the table chromInfo:
## create table from the sql definition
$ hgsql papAnu2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql papAnu2 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
For conditions of use regarding the Baboon genome sequence data, see
http://www.hgsc.bcm.edu/content/conditions-use
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GenBank Data Usage
The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
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All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
gc5BaseBw.txt.gz 2013-01-22 13:01 63
ncbiRefSeqOther.txt.gz 2018-08-14 02:21 75
extNcbiRefSeq.txt.gz 2018-08-14 02:21 90
bigFiles.txt.gz 2024-11-17 03:38 94
grp.txt.gz 2014-03-02 04:14 208
history.txt.gz 2013-01-22 13:01 375
hgFindSpec.txt.gz 2023-12-05 13:51 1.2K
gc5BaseBw.sql 2013-01-22 13:01 1.3K
ncbiRefSeqOther.sql 2018-08-14 02:21 1.3K
ensPep.sql 2018-02-04 08:54 1.3K
grp.sql 2014-03-02 04:14 1.3K
ensemblSource.sql 2018-02-04 08:56 1.4K
ucscToEnsembl.sql 2015-04-13 05:01 1.4K
ncbiRefSeqCds.sql 2018-08-14 02:21 1.4K
bigFiles.sql 2024-11-17 03:38 1.4K
ncbiRefSeqPepTable.sql 2018-08-14 02:21 1.4K
chromInfo.sql 2013-01-22 13:02 1.4K
ensemblToGeneName.sql 2018-02-04 08:57 1.4K
ensGtp.sql 2018-02-04 08:54 1.4K
chromAlias.sql 2018-02-18 08:15 1.4K
tableDescriptions.sql 2024-11-16 02:03 1.4K
ucscToRefSeq.sql 2018-02-18 08:15 1.4K
extNcbiRefSeq.sql 2018-08-14 02:21 1.5K
microsat.sql 2015-08-24 00:04 1.5K
windowmaskerSdust.sql 2013-01-22 13:00 1.5K
cytoBandIdeo.sql 2013-04-28 20:39 1.5K
chainTarSyr2Link.sql 2015-05-25 08:16 1.5K
tableList.sql 2024-11-17 03:38 1.6K
genscanSubopt.sql 2013-01-22 13:01 1.6K
seqNcbiRefSeq.sql 2018-08-14 02:21 1.6K
history.sql 2013-01-22 13:01 1.6K
gap.sql 2013-01-22 13:04 1.6K
gbLoaded.sql 2020-08-22 22:18 1.6K
gold.sql 2013-01-22 13:02 1.7K
genscan.sql 2013-01-22 13:01 1.7K
cpgIslandExt.sql 2013-01-22 12:58 1.7K
chainTarSyr2.sql 2015-05-25 08:21 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 18:39 1.7K
refFlat.sql 2020-08-22 22:18 1.7K
xenoRefFlat.sql 2020-08-22 22:18 1.7K
hgFindSpec.sql 2023-12-05 13:51 1.8K
estOrientInfo.sql 2016-07-10 09:15 1.8K
mrnaOrientInfo.sql 2020-05-08 21:41 1.8K
rmsk.sql 2013-01-22 12:58 1.9K
geneid.sql 2015-11-22 20:32 1.9K
ensGene.sql 2018-02-04 08:56 1.9K
simpleRepeat.sql 2013-01-22 12:58 1.9K
nestedRepeats.sql 2013-01-22 12:58 1.9K
augustusGene.sql 2015-07-26 17:21 1.9K
refGene.sql 2020-08-22 22:18 1.9K
ncbiRefSeq.sql 2018-02-09 13:46 2.0K
xenoRefGene.sql 2020-08-22 22:18 2.0K
ncbiRefSeqCurated.sql 2018-02-09 13:46 2.0K
ncbiRefSeqPredicted.sql 2018-02-09 13:46 2.0K
ncbiRefSeqLink.sql 2018-02-09 13:46 2.0K
trackDb.sql 2023-12-05 13:51 2.1K
netTarSyr2.sql 2015-05-25 08:21 2.1K
all_est.sql 2016-07-10 09:15 2.1K
all_mrna.sql 2020-03-01 08:34 2.1K
intronEst.sql 2016-07-10 09:15 2.1K
xenoMrna.sql 2020-08-22 21:58 2.1K
refSeqAli.sql 2020-05-08 21:41 2.1K
ncbiRefSeqPsl.sql 2018-02-09 13:46 2.1K
xenoRefSeqAli.sql 2020-08-22 22:18 2.1K
tableList.txt.gz 2024-11-17 03:38 3.3K
tableDescriptions.txt.gz 2024-11-16 02:03 6.3K
mrnaOrientInfo.txt.gz 2020-05-08 21:41 17K
trackDb.txt.gz 2023-12-05 13:51 31K
ncbiRefSeqCurated.txt.gz 2018-02-09 13:46 38K
all_mrna.txt.gz 2020-03-01 08:34 38K
gbLoaded.txt.gz 2020-08-22 22:18 41K
refFlat.txt.gz 2020-08-22 22:18 41K
refGene.txt.gz 2020-08-22 22:18 45K
refSeqAli.txt.gz 2020-05-08 21:41 47K
ensemblSource.txt.gz 2018-02-04 08:56 93K
ensemblToGeneName.txt.gz 2018-02-04 08:57 156K
ncbiRefSeqCds.txt.gz 2018-08-14 02:21 194K
ucscToEnsembl.txt.gz 2015-04-13 05:01 299K
chromInfo.txt.gz 2013-01-22 13:02 300K
ensGtp.txt.gz 2018-02-04 08:54 302K
cytoBandIdeo.txt.gz 2013-04-28 20:39 308K
microsat.txt.gz 2015-08-24 00:04 314K
ucscToRefSeq.txt.gz 2018-02-18 08:15 454K
seqNcbiRefSeq.txt.gz 2018-08-14 02:21 504K
cpgIslandExt.txt.gz 2013-01-22 12:58 597K
chromAlias.txt.gz 2018-02-18 08:15 615K
ncbiRefSeqLink.txt.gz 2018-02-09 13:46 964K
gold.txt.gz 2013-01-22 13:02 1.0M
estOrientInfo.txt.gz 2016-07-10 09:15 1.7M
cpgIslandExtUnmasked.txt.gz 2014-06-01 18:39 1.7M
gap.txt.gz 2013-01-22 13:04 1.7M
augustusGene.txt.gz 2015-07-26 17:21 1.9M
geneid.txt.gz 2015-11-22 20:32 2.1M
ensGene.txt.gz 2018-02-04 08:56 2.3M
ncbiRefSeqPredicted.txt.gz 2018-02-09 13:46 2.5M
ncbiRefSeq.txt.gz 2018-02-09 13:46 2.5M
genscan.txt.gz 2013-01-22 13:01 2.5M
ncbiRefSeqPsl.txt.gz 2018-02-09 13:46 2.8M
intronEst.txt.gz 2016-07-10 09:15 3.1M
genscanSubopt.txt.gz 2013-01-22 13:01 5.9M
all_est.txt.gz 2016-07-10 09:15 6.2M
ncbiRefSeqPepTable.txt.gz 2018-08-14 02:21 6.4M
ensPep.txt.gz 2018-02-04 08:54 6.4M
nestedRepeats.txt.gz 2013-01-22 12:58 18M
simpleRepeat.txt.gz 2013-01-22 12:58 29M
xenoRefFlat.txt.gz 2020-08-22 22:18 33M
xenoRefSeqAli.txt.gz 2020-08-22 22:18 35M
xenoRefGene.txt.gz 2020-08-22 22:18 36M
netTarSyr2.txt.gz 2015-05-25 08:21 71M
chainTarSyr2.txt.gz 2015-05-25 08:21 129M
rmsk.txt.gz 2013-01-22 12:58 137M
windowmaskerSdust.txt.gz 2013-01-22 13:00 144M
xenoMrna.txt.gz 2020-08-22 21:58 344M
chainTarSyr2Link.txt.gz 2015-05-25 08:18 832M